Contacts of the strand formed by residues 699 - 706 (chain B) in PDB entry 1QAS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 699 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565B VAL* 4.6 5.8 - - + -
568B TRP* 4.4 13.9 - - + -
588B VAL* 3.9 20.9 - - + +
592B CYS* 3.8 31.9 - - + +
659B GLU 3.7 0.3 - - - +
660B ILE* 3.5 3.6 - - - +
661B HIS* 2.7 43.3 + - + +
697B LEU 4.2 8.3 - - - +
698B ALA* 1.3 82.2 - - - +
700B VAL* 1.3 65.2 + - - +
701B ARG 4.0 0.4 + - - -
720B THR* 3.7 26.9 - - + -
721B ILE 3.4 7.6 - - - +
722B PRO* 4.0 16.4 - - + -
723B TRP 4.0 1.3 - - - +
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Residues in contact with VAL 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631B LEU* 4.0 11.0 - - + -
633B VAL* 5.1 1.3 - - + -
658B VAL* 4.2 14.1 - - + -
659B GLU 3.5 8.1 - - - +
660B ILE* 3.4 25.4 - - + -
699B LEU* 1.3 74.2 - - - +
701B ARG* 1.3 61.0 + - - +
702B PHE* 3.9 29.5 - - + -
719B SER 4.2 0.7 - - - +
720B THR* 3.6 1.2 - - - -
721B ILE* 2.8 44.3 + - - +
723B TRP* 4.1 13.5 - - + -
726B LEU* 4.0 27.6 - - + -
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Residues in contact with ARG 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B PRO* 3.9 23.6 - - - +
587B ASP* 2.6 31.0 + - - +
588B VAL* 4.1 9.0 - - - -
657B ILE 3.7 0.2 - - - +
658B VAL* 3.4 5.9 - - - +
659B GLU* 2.6 85.8 + - + +
661B HIS* 3.8 15.3 - - + -
699B LEU 4.0 0.2 + - - -
700B VAL* 1.3 74.2 - - - +
702B PHE* 1.3 67.4 + - - +
703B MET* 3.4 32.4 - - - +
715B PHE* 4.2 5.3 - - - -
718B GLN* 2.9 20.9 - - - +
719B SER 3.4 6.7 - - - +
720B THR* 3.2 21.5 - - + +
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Residues in contact with PHE 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B ALA* 5.2 0.2 - - + -
633B VAL* 3.7 30.5 - - + -
635B ILE* 4.1 17.7 - - + -
656B VAL* 4.9 0.7 - - + -
657B ILE 3.6 3.4 - - - -
658B VAL* 4.1 8.7 - - + -
700B VAL* 3.9 29.2 - - + -
701B ARG* 1.3 74.0 - - - +
703B MET* 1.3 61.1 + - - +
704B VAL* 5.3 1.3 - - - -
718B GLN* 3.3 6.8 - - - +
719B SER 2.8 36.0 + - - +
721B ILE* 3.8 23.8 - - + -
726B LEU* 4.3 12.3 - - + -
733B VAL* 4.1 42.2 - - + -
735B LEU* 4.8 1.5 - - + +
748B LEU* 4.3 12.6 - - + -
750B VAL* 4.5 2.7 - - + -
752B ILE* 4.7 7.6 - - + -
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Residues in contact with MET 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B PRO* 6.2 1.8 - - + -
655B LYS 3.6 0.7 - - - +
656B VAL* 3.1 5.7 - - - +
657B ILE* 2.6 64.0 + - + +
659B GLU* 5.0 3.4 - - - +
701B ARG* 3.4 42.0 - - + +
702B PHE* 1.3 72.9 - - - +
704B VAL* 1.3 68.4 + - - +
705B GLU* 3.7 36.1 - - + +
715B PHE* 4.1 22.2 - - - -
717B GLY 4.0 1.1 - - - -
718B GLN* 4.0 5.6 - - + -
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Residues in contact with VAL 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641B LEU* 4.1 20.6 - - + -
654B PRO* 4.2 5.6 - - + -
655B LYS 3.3 11.9 - - - +
656B VAL* 4.2 9.0 - - + -
703B MET* 1.3 80.1 - - - +
705B GLU* 1.3 61.1 - - - +
715B PHE* 3.9 2.3 - - - -
716B ILE* 2.8 45.5 + - + +
717B GLY 3.0 14.9 + - - +
735B LEU* 3.8 30.1 - - + -
748B LEU* 3.8 26.5 - - + -
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Residues in contact with GLU 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654B PRO* 3.3 7.4 - - - +
655B LYS* 2.9 42.5 + - + +
657B ILE* 3.6 25.0 - - + +
703B MET* 3.7 22.7 - - + +
704B VAL* 1.3 76.5 - - - +
706B ASP* 1.3 62.1 + - - +
707B TYR 3.7 0.4 + - - -
712B LYS* 3.6 21.7 + - - -
713B ASN* 2.8 37.5 + - + +
714B ASP 3.4 10.1 - - - +
715B PHE* 4.9 1.8 - - - -
716B ILE* 3.4 6.8 - - - +
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Residues in contact with ASP 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644B VAL* 3.6 14.7 - - + +
651B ILE 4.5 2.3 - - - +
652B VAL* 3.2 23.6 - - - +
653B ASP* 3.1 28.3 + - - +
705B GLU* 1.3 73.1 - - - +
707B TYR* 1.3 68.3 + - - +
708B ASP* 6.2 0.2 - - - -
713B ASN* 3.0 7.1 - - - -
714B ASP* 2.6 56.3 + - + +
716B ILE* 3.9 11.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il